Well yes, you would have an idea where the ship was a few minutes ago, and in FreeSpace, that doesn't cut it.
Within a few minutes, the ship could have jumped to an infinite number of other locations in system. Given that it keeps jumping around like that, you could know its there, but you wouldn't know where it is, nor where it is going. Well, unless you track it through subspace, but given that you have never actually seen what it is before, I don't know if that is possible.
The principle that there can be no stealth in space is because without subspace, craft can only travel in essentially a linear fashion, allowing you to pretty much calculate where the ship will end up.